Skip to main content
!
Phase III Operations: The University is open for expanded research operations; only authorized personnel will be admitted on campus. More info here.

Publications search

Found 35038 matches. Displaying 11-20
Chang JWC, Shih CL, Wang CL, Luo JD, Wang CW, Hsieh JJ, Yu CJ, Chiou CC
Show All Authors

Transcriptomic Analysis in Liquid Biopsy Identifies Circulating PCTAIRE-1 mRNA as a Biomarker in NSCLC

CANCER GENOMICS & PROTEOMICS 2020 JAN-FEB; 17(1):91-100
Background/Aim: Circulating mRNA can be a useful source of cancer biomarkers. We took advantage of direct transcriptomic analysis in plasma RNA to identify novel mRNA markers for non-small cell lung cancer (NSCLC). Patients and Methods: Plasma RNA from NSCLC patients and healthy individuals was profiled with cDNA-mediated annealing, selection, extension and ligation (DASL) microarrays. The microarray results were further validated in plasma RNA. Results: Through RNA profiling and online database mining, four gene transcripts were filtered as candidate markers of NSCLC. After validation, the PCTAIRE-1 transcript was identified as a circulating mRNA marker. The diagnostic potential of PCTAIRE-1 was evaluated by receiver operating characteristic curve analysis, which gave a sensitivity and specificity of 60% and 85%, respectively. In addition, high plasma PCTK1 levels were also correlated with poor progression free survival (p=0.008). Conclusion: Circulating mRNA can be profiled with the DASL assay. From the profile, PCTAIRE-1 RNA in the plasma we discovered as a novel diagnostic/prognostic biomarker and an indicator of poor survival in NSCLC patients.
Donovan FX, Solanki A, Mori M, Chavan N, George M, Kumar CS, Okuno Y, Muramastsu H, Yoshida K, Shimamoto A, Takaori-Kondo A, Yabe H, Ogawa S, Kojima S, Yabe M, Ramanagoudr-Bhojappa R, Smogorzewska A, Mohan S, Rajendran A, Auerbach AD, Takata M, Chandrasekharappa SC, Vundinti BR
Show All Authors

A founder variant in the South Asian population leads to a high prevalence of FANCL Fanconi anemia cases in India

HUMAN MUTATION 2020 JAN; 41(1):122-128
Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure, predisposition to cancer, and congenital abnormalities. FA is caused by pathogenic variants in any of 22 genes involved in the DNA repair pathway responsible for removing interstrand crosslinks. FANCL, an E3 ubiquitin ligase, is an integral component of the pathway, but patients affected by disease-causing FANCL variants are rare, with only nine cases reported worldwide. We report here a FANCL founder variant, anticipated to be synonymous, c.1092G>A;p.K364=, but demonstrated to induce aberrant splicing, c.1021_1092del;p.W341_K364del, that accounts for the onset of FA in 13 cases from South Asia, 12 from India and one from Pakistan. We comprehensively illustrate the pathogenic nature of the variant, provide evidence for a founder effect, and propose including this variant in genetic screening of suspected FA patients in India and Pakistan, as well as those with ancestry from these regions of South Asia.
Galea S, Vaughan RD
Show All Authors

The Future of a Public Health of Consequence: A Public Health of Consequence, December 2019

AMERICAN JOURNAL OF PUBLIC HEALTH 2019 DEC; 109(12):1628-1629
Gur-Cohen S, Yang H, Baksh SC, Miao YX, Levorse J, Kataru RP, Liu XL, de la Cruz-Racelis J, Mehrara BJ, Fuchs E
Show All Authors

Stem cell-driven lymphatic remodeling coordinates tissue regeneration

SCIENCE 2019 DEC 6; 366(6470):1218-1225
Tissues rely on stem cells (SCs) for homeostasis and wound repair. SCs reside in specialized microenvironments (niches) whose complexities and roles in orchestrating tissue growth are still unfolding. Here, we identify lymphatic capillaries as critical SC-niche components. In skin, lymphatics form intimate networks around hair follicle (HF) SCs. When HFs regenerate, lymphatic-SC connections become dynamic. Using a mouse model, we unravel a secretome switch in SCs that controls lymphatic behavior. Resting SCs express angiopoietin-like protein 7 (Angptl7), promoting lymphatic drainage. Activated SCs switch to Angptl4, triggering transient lymphatic dissociation and reduced drainage. When lymphatics are perturbed or the secretome switch is disrupted, HFs cycle precociously and tissue regeneration becomes asynchronous. In unearthing lymphatic capillaries as a critical SC-niche element, we have learned how SCs coordinate their activity across a tissue.
Galea S, Vaughan RD
Show All Authors

ETHICAL REFLECTION IS ESSENTIAL FOR PUBLIC HEALTH AND IS NOT THE SAME AS POLITICAL REFLECTION Response

AMERICAN JOURNAL OF PUBLIC HEALTH 2019 DEC; 109(12):E1-E2
Lee CH, MacKinnon R
Show All Authors

Voltage Sensor Movements during Hyperpolarization in the HCN Channel

CELL 2019 DEC 12; 179(7):1582-1589.e7
The hyperpolarization-activated cyclic nucleotidegated (HCN) channel is a voltage-gated cation channel that mediates neuronal and cardiac pacemaker activity. The HCN channel exhibits reversed voltage dependence, meaning it closes with depolarization and opens with hyperpolarization. Different from Na+, Ca2+, and Kv1-Kv7 channels, the HCN channel does not have domain-swapped voltage sensors. We introduced a reversible, metal-mediated cross bridge into the voltage sensors to create the chemical equivalent of a hyperpolarized conformation and determined the structure using cryoelectron microscopy (cryo-EM). Unlike the depolarized HCN channel, the S4 helix is displaced toward the cytoplasm by two helical turns. Near the cytoplasm, the S4 helix breaks into two helices, one running parallel to the membrane surface, analogous to the S4-S5 linker of domain-swapped voltage-gated channels. These findings suggest a basis for allosteric communication between voltage sensors and the gate in this kind of channel. They also imply that voltage sensor movements are not the same in all voltage-gated channels.
Capoor MN, Birkenmaier C, Wang JC, McDowell A, Ahmed FS, Br?ggemann H, Coscia E, Davies DG, Ohrt-Nissen S, Raz A, Ruzicka F, Schmitz JE, Fischetti VA, Slaby O
Show All Authors

A review of microscopy-based evidence for the association of Propionibacterium acnes biofilms in degenerative disc disease and other diseased human tissue

EUROPEAN SPINE JOURNAL 2019 DEC; 28(12):2951-2971
Purpose Recent research shows an increasing recognition that organisms not traditionally considered infectious in nature contribute to disease processes. Propionibacterium acnes (P. acnes) is a gram-positive, aerotolerant anaerobe prevalent in the sebaceous gland-rich areas of the human skin. A ubiquitous slow-growing organism with the capacity to form biofilm, P. acnes, recognized for its role in acne vulgaris and medical device-related infections, is now also linked to a number of other human diseases. While bacterial culture and molecular techniques are used to investigate the involvement of P. acnes in such diseases, definitive demonstration of P. acnes infection requires a technique (or techniques) sensitive to the presence of biofilms and insensitive to the presence of potential contamination. Fortunately, there are imaging techniques meeting these criteria, in particular, fluorescence in situ hybridization and immunofluorescence coupled with confocal laser scanning microscopy, as well as immunohistochemistry. Methods Our literature review considers a range of microscopy-based studies that provides definitive evidence of P. acnes colonization within tissue from a number of human diseases (acne vulgaris, degenerative disc and prostate disease and atherosclerosis), some of which are currently not considered to have an infectious etiology. Results/Conclusion We conclude that P. acnes is an opportunistic pathogen with a likely underestimated role in the development of various human diseases associated with significant morbidity and, in some cases, mortality. As such, these findings offer the potential for new studies aimed at understanding the pathological mechanisms driving the observed disease associations, as well as novel diagnostic strategies and treatment strategies, particularly for degenerative disc disease. Graphic abstract These slides can be retrieved under Electronic Supplementary Material.
Tao X, MacKinnon R
Show All Authors

Molecular structures of the human Slo1 K+ channel in complex with beta 4

ELIFE 2019 DEC 9; 8(?):? Article e51409
Slo1 is a Ca2+- and voltage-activated K+ channel that underlies skeletal and smooth muscle contraction, audition, hormone secretion and neurotransmitter release. In mammals, Slol is regulated by auxiliary proteins that confer tissue-specific gating and pharmacological properties. This study presents cryo-EM structures of Slo1 in complex with the auxiliary protein, beta 4. Four beta 4, each containing two transmembrane helices, encircle Slot, contacting it through helical interactions inside the membrane. On the extracellular side, beta 4 forms a tetrameric crown over the pore. Structures with high and low Ca(2+ )concentrations show that identical gating conformations occur in the absence and presence of beta 4, implying that beta 4 serves to modulate the relative stabilities of 'pre-existing' conformations rather than creating new ones. The effects of beta 4 on scorpion toxin inhibition kinetics are explained by the crown, which constrains access but does not prevent binding.
Minis A, Rodriguez JA, Levin A, Liu K, Govek EE, Hatten ME, Steller H
Show All Authors

The proteasome regulator PI31 is required for protein homeostasis, synapse maintenance, and neuronal survival in mice

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2019 DEC 3; 116(49):24639-24650
Proteasome-mediated degradation of intracellular proteins is essential for cell function and survival. The proteasome-binding protein PI31 (Proteasomal Inhibitor of 31kD) promotes 265 assembly and functions as an adapter for proteasome transport in axons. As localized protein synthesis and degradation is especially critical in neurons, we generated a conditional loss of PI31 in spinal motor neurons (MNs) and cerebellar Purkinje cells (PCs). A cKO of PI31 in these neurons caused axon degeneration, neuronal loss, and progressive spinal and cerebellar neurological dysfunction. For both MNs and PCs, markers of proteotoxic stress preceded axonal degeneration and motor dysfunction, indicating a critical role for PI31 in neuronal homeostasis. The time course of the loss of MN and PC function in developing mouse central nervous system suggests a key role for PI31 in human neurodegenerative diseases.
Bohn JA, DaSilva J, Kharytonchyk S, Mercedes M, Vosters J, Telesnitsky A, Hatziioannou T, Smith JL
Show All Authors

Flexibility in Nucleic Acid Binding Is Central to APOBEC3H Antiviral Activity

JOURNAL OF VIROLOGY 2019 DEC; 93(24):? Article e01275-19
APOBEC3 proteins APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H) are host restriction factors that inhibit HIV-1 through DNA cytidine deaminasedependent and -independent mechanisms and have either one (A3H) or two (A3F and A3G) zinc-binding domains. A3H antiviral activity encompasses multiple molecular functions, all of which depend on recognition of RNA or DNA. A3H crystal structures revealed an unusual interaction with RNA wherein an RNA duplex mediates dimerization of two A3H proteins. In this study, we sought to determine the importance of RNAbinding amino acids in the antiviral and biochemical properties of A3H. We show that the wild-type A3H-RNA interaction is essential for A3H antiviral activity and for two deaminase-independent processes: encapsidation into viral particles and inhibition of reverse transcription. Furthermore, an extensive mutagenesis campaign revealed distinct roles for two groups of amino acids at the RNA binding interface. C-terminal helix residues exclusively bind RNA, and loop 1 residues play a dual role in recognition of DNA substrates and in RNA binding. Weakening the interface between A3H and RNA allows DNA substrates to bind with greater affinity and enhances deamination rates, suggesting that RNA binding must be disrupted to accommodate DNA. Intriguingly, we demonstrate that A3H can deaminate overhanging DNA strands of RNA/DNA heteroduplexes, which are early intermediates during reverse transcription and may represent natural A3H substrates. Overall, we present a mechanistic model of A3H restriction and a step-by-step elucidation of the roles of RNA-binding residues in A3H activity, particle incorporation, inhibition of reverse transcriptase inhibition, and DNA cytidine deamination. IMPORTANCE APOBEC3 proteins are host factors that protect the integrity of the host genome by inhibiting retroelements as well as retroviruses, such as HIV-1. To do this, the APOBEC3H protein has evolved unique interactions with structured RNAs. Here, we studied the importance of these interactions in driving antiviral activity of APOBEC3H. Our results provide a clear picture of how RNA binding drives the ability of APOBEC3H to infiltrate new viruses and prevent synthesis of viral DNA. We also explore how RNA binding by APOBEC3H influences recognition and deamination of viral DNA and describe two possible routes by which APOBEC3H might hypermutate the HIV-1 genome. These results highlight how one protein can sense many nucleic acid species for a variety of antiviral activities.